The "lipochrome, recessive" thing drives me NUTS because that is a real eye color! That's an eye color real people right now have. About 5% of the world's population have amber eyes, eyes that appear to be golden, yellow, or copper in color, pigmented by lipochrome.
So I guess Cytherea assumed the yellow was John's natural eye color, after she saw his daughter had inherited it. It wouldn't be weird for Wake to be a carrier for the phenotype while having darker eyes herself, since it's a recessive trait. Like John must be a carrier for red hair, for Gideon to have inherited that from Wake. Meanwhile we now know something Cytherea doesn't: the yellow isn't natural lipochromatic pigment at all, it's magical girl bullshit! So it's entirely probable the eyes came with whatever power made little baby Gideon not die when she was killed, and Cytherea used the wrong equation to get the right answer.
I would LOVE to confirm if Babs' eyes changed color too. Unlike John, Ianthe didn't put any of herself into her cavalier. She just slurped Babs' soul up and swallowed it whole. So would the eye color be a two-way swap for that kind of lyctorhood? If Harrow hadn't been able to save Gideon, would the dull clouded eyes on Gideon's corpse have been black or gold?
Swerving away from the eye color thing for a minute, there is a lot to explore in that last paragraph of your first reply!
First off, I'm not sure if we have enough information to conclude that all lyctors are sterile. It'd make sense if lyctorhood fucked with reproduction, since necromancy sure does, but we don't really know why all of Mercy's eggs died. It could be that lyctors are reproductively incompatible with John specifically; or it could be just be something to do with Mercymorn, and not her lyctorhood. Totally a good theory, and I think you may be right, but more research needed before Pyrrha and/or Paul can start counting on lyctorhood as birth control.
As to the lyctors having had tons of children before they ascended: I suppose it's possible, but I doubt it. No House other than the Ninth has been established as tracing their genetic lineage back to a founding ancestor, and I have trouble imagining that of Mercymorn or Gideon the First. Totally see where you're getting the correlation between lyctor and House, with Ninth eyes and Cytherea saying that "the Seventh House is awfully predictable for looks," but Cytherea didn't found the Seventh. She was born there, meaning she had family there. She doesn't need to have personally contributed anything to that gene pool for a passable look-alike to pop up millenia later.
I'm kind of hesitant about assuming all the Houses have distinctive phenotypes. It's been implied some other stereotypes exist in the setting, like Silas wondering if Gideon's mother had been Third because of their hair, but Silas was being a creep when he said that, and he was wrong besides. It's not the kind of world building I want to lean into. Protesilaus and Dulcinea look nothing alike, despite what Cytherea said, and the necrocav pairs that do look alike also tend to be fairly closely related and thus not a good measure for the House as a whole. Our sample size is small, our standard deviation is high, ect.
Some of the disciples having had children, tho, whose descendants they watched live and die through generations? That is a fascinating idea, and I'd love to explore it. Would their descendants know? If yes, do the other Houses have heroes they claim are descended from lyctors? Were Anastasia's children still young when she built the Tomb, or was she already the grandmother of the Ninth, ancestor of her people? John kept his disciples young and immortal for centuries, but only if they stayed close to him. Was Anastasia having a family part of the original push for an independent lyctorhood?
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